Hey Pete491,
The bindings file is in your /user/appdata folder. I'm not in front of my rig at the moment, so I can't tell you specifically, but there'll be two Frontier folders in the appdata/local. The appdata folder is hidden by default, so you'll have to make it visible simply type it into the address field. I've run into similar problems before, and all I did was make a directory within the /bindings directory called /backups. Once I have my setup as I like it, I save them and get out of the game. I then navigate to the folder and copy everything in the /bindings directory into the backup directory (excluding the actual backup directory itself ;P ). If anything ever happens, much like what happened to you, I simply copy the file from the /backup into the /bindings and I'm good to go again.
That being said, if you ever find yourself making changes to the key bindings, make sure to copy your new bindings file into the /backup directory.
As to your original question as to "how could this happen," it could be any number of things. In my case, simply because my pedals weren't recognized by my rig, ALL my bindings didn't work. Another way my bindings are recognized is if I forget to initialize the T.A.R.G.E.T. software that came with my HOTAS. In both cases, however, my bindings file wasn't corrupted, only not read in because ED thought the setup was different. Simply fixing the issue and getting back into ED was all that was required. You mileage may vary, though.
Guys,
For some reason after I made a change to my key bindings I lost all of my settings. Bummer!! No idea how this happened. Lot's of time setting this up. Any idea how this could have happened? What is the name of the file that contains these. Maybe I can get them from a backup.
Thanks!